gseaScores

Calculate GSEA Running Enrichment Scores

Fast implementations of functional enrichment analysis methods using 'C++' via 'Rcpp'.
Currently provides Over-Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA).
The multilevel GSEA algorithm is derived from the 'fgsea' package.
Methods are described in Subramanian et al. (2005) <doi:10.1073/pnas.0506580102> and Korotkevich et al. (2021) <doi:10.1101/060012>.

Guangchuang Yu

enrichit

'C++' Implementations of Functional Enrichment Analysis

gseaScores function

<dl><dt>geneList</dt>
<dd>a named numeric vector of gene statistics (e.g., t-statistics or log-fold changes), sorted in decreasing order.</dd>
<dt>geneSet</dt>
<dd>a character vector of gene IDs belonging to the gene set.</dd>
<dt>exponent</dt>
<dd>a numeric value defining the weight of the running enrichment score. Default is 1.</dd>
<dt>fortify</dt>
<dd>logical. If TRUE, returns a data frame with columns <code>x</code>, <code>runningScore</code>, and <code>position</code>.
If FALSE (default), returns the enrichment score (ES).</dd></dl>

Arguments

Author

Calculate GSEA Running Enrichment Scores — gseaScores

<dl>

<dt>geneList</dt>
<dd>a named numeric vector of gene statistics (e.g., t-statistics or log-fold changes), sorted in decreasing order.</dd>


<dt>geneSet</dt>
<dd>a character vector of gene IDs belonging to the gene set.</dd>


<dt>exponent</dt>
<dd>a numeric value defining the weight of the running enrichment score. Default is 1.</dd>


<dt>fortify</dt>
<dd>logical. If TRUE, returns a data frame with columns <code>x</code>, <code>runningScore</code>, and <code>position</code>.
If FALSE (default), returns the enrichment score (ES).</dd>

</dl>

gseaScores: Calculate GSEA Running Enrichment Scores

Description

Usage

Value

Arguments

Author